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The C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J31
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 2.5-4.0 mg/ml protein, 0.1 M Imidazole, MES monohydrate (acid) buffer at pH 6.5, 20% v/v Glycerol, 10% w/v PEG 4000, 0.2M Glutaramide
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.684 α = 90 b = 100.639 β = 90 c = 134.096 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2010-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 1.0000 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.58 100.64 100 0.125 0.042 8.8 8.8 144086 18.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.61 99.8 2.971 1.036 0.4 8.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1j31 1.58 80.492 1.33 143188 7145 99.37 0.2082 0.2065 0.2068 0.2398 0.2398 31.1176
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8497 Nucleic Acid Atoms Solvent Atoms 556 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction DIALS data reduction